NAME

Bio::Tools::Run::PiseApplication::polydot

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::polydot

      Bioperl class for:

	POLYDOT	Displays all-against-all dotplots of a set of sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/polydot.html 
         for available values):


		polydot (String)

		init (String)

		sequences (Sequence)
			Sequences file to be read in (-sequences)
			pipe: seqsfile

		wordsize (Integer)
			Word size (-wordsize)

		data (Switch)
			Display as data (-data)

		graph (Excl)
			graph [device to be displayed on] (-graph)

		outfile (OutFile)
			outfile (-outfile)

		gap (Integer)
			Gap (in residues) between dotplots (-gap)

		boxit (Switch)
			Draw a box around each dotplot (-boxit)

		dumpfeat (Switch)
			Dump all matches as feature files (-dumpfeat)

		format (String)
			format to Dump out as (-format)

		ext (String)
			Extension for feature file (-ext)

		auto (String)

		psouput (String)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/polydot.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $polydot = Bio::Tools::Run::PiseApplication::polydot->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::polydot object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $polydot = $factory->program('polydot');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::polydot.